Adsorption energy of protein in vacuum

From: Madhulika Gupta (
Date: Fri May 20 2016 - 06:01:05 CDT

Dear All,
I am trying to study protein adsorption on metal surface in vacuum in NAMD.
I am getting almost double the adsorption energies values as that in
explicit water and DFT studies.
I am not sure if there is a different method to treat electrostatics and
van der Waal forces in vacuum. I am using PME off and a cutoff of 12 A for
45X45X45 A box.
Please advise as to how should I modify the vacuum simulations to get
better results in namd?

Thanks and Regards

Madhulika Gupta
Research Scholar
Department of Chemistry
Indian Institute of Technology, Delhi
New Delhi-110016

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